Shannon log(Observed)
India 0.0099 0.0013
India (exposed) 0.3155 0.2959
India (unexposed) 0.0036 0.0001
Malawi 0.5418 0.5263
UK 0.8155 0.5826
India India_exposed India_unexposed Malawi UK
Shannon -0.0194 0.0807 -0.1688 -0.3269 -0.0364
log(richness) -0.0538 0.0569 -0.1795 -0.2933 -0.0929
India India_exposed India_unexposed Malawi UK
Shannon 0.7429 0.3201 0.0530 0.0074 0.8061
log(richness) 0.3640 0.4834 0.0394 0.0169 0.5300
India India_exposed India_unexposed Malawi UK
Shannon -0.0476 -0.0429 -0.0432 0.0767 -0.0630
log(richness) -0.0483 0.0600 -0.0950 -0.0380 0.0067
India India_exposed India_unexposed Malawi UK
Shannon 0.4272 0.5903 0.6393 0.5852 0.6670
log(richness) 0.4198 0.4507 0.3022 0.7870 0.9635
Shannon log(Observed)
India 0.1704 0.1318
India (exposed) 0.8656 0.6844
India (unexposed) 0.2384 0.0572
Malawi 0.2673 0.1553
Shannon log(Observed)
India 0.3228 0.1297
India (exposed) 0.9722 0.6468
India (unexposed) 0.3455 0.1966
Malawi 0.9498 0.4796
Shannon log(Observed)
India 0.4005 0.5271
See Module 5 for full univariate and multivariate analyses.
Shannon_rsv log(Observed_rsv)
India 0.0182 0.0044
India (exposed) 0.2923 0.3252
India (unexposed) 0.0156 0.0012
Malawi 0.9276 0.8659
UK 0.9307 0.5172
India India_exposed India_unexposed Malawi UK
Shannon 0.0032 0.0729 -0.1138 -0.1374 -0.1349
log(richness) -0.0555 0.0416 -0.2035 -0.1915 -0.0843
India India_exposed India_unexposed Malawi UK
Shannon 0.9568 0.3690 0.1940 0.2711 0.3608
log(richness) 0.3487 0.6083 0.0192 0.1235 0.5689
India India_exposed India_unexposed Malawi UK
Shannon -0.0254 -0.0476 0.0746 0.0942 -0.0103
log(richness) -0.0398 0.0065 -0.0616 -0.0251 -0.0544
India India_exposed India_unexposed Malawi UK
Shannon 0.6712 0.5502 0.4181 0.5023 0.9438
log(richness) 0.5062 0.9349 0.5036 0.8583 0.7107
Shannon_rsv log(Observed_rsv)
India 0.5308 0.3872
India (exposed) 0.8026 0.6590
India (unexposed) 0.6945 0.2629
Malawi 0.1322 0.1664
Shannon_rsv log(Observed_rsv)
India 0.9686 0.3633
India (exposed) 0.8933 0.6198
India (unexposed) 0.9022 0.6262
Malawi 0.7173 0.9673
Shannon_rsv log(Observed_rsv)
India 0.8768 0.64
negatively correlated ns positively correlated
age 6 12 7
IgA 0 25 0
seroconv 0 25 0
[1] "No significant differences according to ORV outcome"
negatively correlated ns positively correlated
age 7 11 8
IgA 1 25 0
seroconv 0 26 0
taxon Estimate Std.Error padj comparison mean prev
59 Lactobacillus -0.181 0.055 0.0364 IgA 3.685 62.7
negatively correlated ns positively correlated
age 6 10 8
IgA 0 24 0
seroconv 0 24 0
[1] "No significant differences according to ORV outcome"
negatively correlated ns positively correlated
age 12 14 15
IgA 0 41 0
seroconv 0 41 0
[1] "No significant differences according to ORV outcome"
negatively correlated ns positively correlated
age 13 8 4
IgA 0 24 0
seroconv 0 25 0
taxon Estimate Std.Error padj comparison
2 Escherichia/Shigella 0.045 0.013 1.727273e-03 age
3 Streptococcus -0.119 0.024 5.312500e-06 age
4 Staphylococcus -0.435 0.025 1.825000e-35 age
7 Lactobacillus -0.068 0.035 7.812500e-02 age
8 Collinsella -0.024 0.013 7.941176e-02 age
9 Haemophilus -0.226 0.023 1.125000e-16 age
10 Klebsiella -0.156 0.020 3.125000e-12 age
11 Enterococcus -0.116 0.024 1.194444e-05 age
14 Gemella -0.120 0.020 3.250000e-08 age
15 Enterobacter -0.050 0.017 7.142857e-03 age
16 Parabacteroides -0.051 0.016 2.500000e-03 age
17 Corynebacterium_1 -0.164 0.023 1.666667e-10 age
20 Granulicatella -0.063 0.015 1.225000e-04 age
22 Actinomyces -0.234 0.032 5.500000e-11 age
23 Eggerthella 0.146 0.018 1.916667e-12 age
24 Negativicoccus 0.058 0.021 1.016667e-02 age
25 Prevotella 0.256 0.078 2.500000e-03 age
[1] "No significant differences according to ORV outcome"
ns
dose1 23
[1] "No significant differences according to ORV outcome"
ns
dose1 24
[1] "No significant differences according to ORV outcome"
ns
dose1 22
[1] "No significant differences according to ORV outcome"
negatively correlated ns
dose1 1 41
taxon Estimate Std.Error padj comparison mean prev
28 Sutterella -1.418 0.369 0.00966 dose1 1.28 43.9
negatively correlated ns
either 2 21
taxon Estimate Std.Error padj comparison mean prev
17 Corynebacterium_1 -0.342 0.110 0.02415 either 0.022 65.5
22 Dolosigranulum -1.069 0.339 0.02415 either 0.012 35.4
ns
either 24
[1] "No significant differences according to ORV outcome"
negatively correlated ns
either 1 21
taxon Estimate Std.Error padj comparison mean prev
17 Corynebacterium_1 -0.769 0.246 0.0462 either 0.024 66.8
negatively correlated ns positively correlated
either 2 36 4
taxon Estimate Std.Error padj comparison mean prev
9 Haemophilus 1.430 0.461 0.084 either 0.404 40.0
10 Klebsiella 1.571 0.611 0.084 either 3.946 70.4
14 Gemella 0.919 0.351 0.084 either 0.029 64.4
26 Phascolarctobacterium 1.769 0.644 0.084 either 0.169 27.4
31 Holdemanella -1.701 0.569 0.084 either 0.172 28.1
36 Lawsonella -2.512 0.933 0.084 either 0.007 22.2
.